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Rhizoctonia root and hypocolyl rot, caused by Rhizoctonia solani Kuhn [teleomorph Thanatephorus cucumeris (Frank) Donk], is an important disease of soybean [Glycine max (L.) Merr.]. Planting resistant cultivars would be an effective and environmentally sound strategy to minimize economic losses from this disease. To facilitate developing resistant cultivars, a study was conducted to: (i) investigate inheritance of resistance to Rhizoctonia root and hypocotyl rot in the moderately resistant soybean PI 442031, and four moderately susceptible commercial cultivars and (ii) identify simple sequence repeat (SSR) markers associated with resistance to Rhizoctonia root and hypocotyl rot. Genetic analysis of several segregating populations indicated that resistance to Rhizoctonia root and hypocotyl rot in soybean was quantitatively inherited and controlled by both major and minor genes with additive gene effects. The estimates of broad sense heritability of resistance were low to moderately high. Transgressive segregants with enhanced levels of resistance were developed by crossing adapted but moderately susceptible commercial soybean cultivars. Three SSR markers (Satt281, Satt177, and Satt245) were significantly associated with host resistance in both [F.sub.2] and [F.sub.4:5] populations of PI 442031 x Sterling, wherein both parents contributed resistant alleles. This is the first report on mapping of Rhizoctonia root and hypocotyl rot resistance genes in soybean. Our results indicate that marker assisted selection, coupled with phenotypic selection in later generations, should help to facilitate the development of soybean cultivars resistant to Rhizoctonia root and hypocotyl rot., RHIZOCTONIA ROOT AND HYPOCOTYL ROT is a major disease of soybean (Sinclair and Dhingra, 1975; Yang, 1999). Rhizoctonia solani is predominantly soilborne with a wide host range (Menzies, 1970), making [...]

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The article discusses the results of a study that examined the predominant species of Diaporthe and Phomopsis occurring in soybean plants and seeds in Ontario. The study also examined the benefits of fungicidal seed treatments and biocontrol agents applied alone or combined. The researchers found that fludioxonil, difenoconazole, triazolinthion and trifloxystrobin protect soybean from Diaporthe and Phomopsis.

Studies the anastomosis groups of Rhizoctonia solani associated with soybean root and hypocotyl rot in Ontario and resistance of accession PI 442032 to different anastomosis group (AG). Nuclear number and anastomosis grouping; Isolation of genomic DNA; Inoculum production and inoculation.

Genetic interactions for disease response between cultivars of Glycine max and isolates of Sclerotinia sclerotiorum were evaluated in controlled-environment inoculations of five soybean cultivars with four genetically unique isolates of S. sclerotiorum. The objective of this study was to identify host-pathogen interactions using isolates of the pathogen which had different geographical and crop-wise distribution as well as a different DNA-based fingerprint. To do so, 4week-old soybean plants were inoculated with individual isolates of S. sclerotiorum using a straw inoculation method. Inoculated plants were incubated for 48 h in continuous leaf wetness and rated for disease severity 1 and 2 weeks after inoculation. Significant differences in disease severity were detected among the soybean cultivars, and NK S08-80 consistently had the lowest disease severity among the five cultivars tested. No significant differences in disease severity were observed among pathogen isolates and no significant interactions were detected between soybean cultivars and pathogen isolates. These results suggest the following interpretations: (i) either the clonal genotype of the four pathogen isolates as determined by mycelial compatibility and DNA fingerprint was not associated with level of virulence on the five soybean cultivars or (ii) the soybean cultivars themselves were not capable of revealing any differences in virulence among isolates that would be related to their genetic fingerprint or regional distribution. The results of this study are consistent with the practice of considering different isolates of S. sclerotiorum sampled from soybean in the same geographical region as equivalent for the evaluation of soybean cultivars for resistance to Sclerotinia stem rot. [ABSTRACT FROM AUTHOR]

New selection methods, using trait-specific markers (marker-assisted selection (MAS)) and/or genome-wide markers (genomic selection (GS)), are becoming increasingly widespread in breeding programs. This new era requires innovative and cost-efficient solutions for genotyping. Reduction in sequencing cost has enhanced the use of high-throughput low-cost genotyping methods such as genotyping-by-sequencing (GBS) for genome-wide single-nucleotide polymorphism (SNP) profiling in large breeding populations. However, the major weakness of GBS methodologies is their inability to genotype targeted markers. Conversely, targeted methods, such as amplicon sequencing (AmpSeq), often face cost constraints, hindering genome-wide genotyping across a large cohort. Although GBS and AmpSeq data can be generated from the same sample, an efficient method to achieve this is lacking. In this study, we present the Genome-wide & Targeted Amplicon (GTA) genotyping platform, an innovative way to integrate multiplex targeted amplicons into the GBS library preparation to provide an all-in-one cost-effective genotyping solution to breeders and research communities. Custom primers were designed to target 23 and 36 high-value markers associated with key agronomical traits in soybean and barley, respectively. The resulting multiplex amplicons were compatible with the GBS library preparation enabling both GBS and targeted genotyping data to be produced efficiently and cost-effectively. To facilitate data analysis, we have introduced Fast-GBS.v3, a user-friendly bioinformatic pipeline that generates comprehensive outputs from data obtained following sequencing of GTA libraries. This high-throughput low-cost approach will greatly facilitate the application of DNA markers as it provides required markers for both MAS and GS in a single assay., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Euphorbia lagascae Spreng is a promising emerging oilseed crop, with its seed oil accounting for approximately 50% of the seed weight. Euphorbia oil contains a significant amount of vernolic acid, comprising two-thirds of its composition, which boasts various industrial applications, including acting as a stabilizer-plasticizer and natural dye. However, this species was known to have a high degree of seed-shattering and a low germination rate, which act as two important barriers to large-scale production and exploitation. Therefore, the objective of this study is to determine the genetic control of seed germination and seed-shattering traits in order to develop a reliable pipeline that would be applicable for industries and breeders to select superior E. lagascae lines and design a robust breeding scheme in a short time at reduced labor costs. For this objective, five different wild-type genotypes of E. lagascae that demonstrated high germination potential were crossed with an ethyl methanesulfonate (EMS) mutant genotype that produces non-shattering capsules. The F 2 populations from two successful crosses (A and B) were separated into three different treated groups for seed germination evaluation and to study the segregation of 200 individuals per F 2 population. The three treatments were: light, gibberellic acid (GA 3 ), and control treatment. Consequently, plants treated with approximately 250 μmol/m 2 /s of light showed significant improvement in germination up to 75% in cross A and 82.4 % in cross B compared with the control plants and the group treated with 0.05% GA 3 . According to the chi-square test results, the inheritance pattern of seed germination in response to light treatment follows a 3:1 segregation ratio between germinated and non-germinated seeds, indicating a dominant gene action in the F 2 generation. The same conclusion was followed for the shattering trait in the group treated with light, which was also simply inherited as a 3:1 ratio for shattering vs. non-shattering capsules. Our results emphasize the importance and significance of light treatment in producing uniform populations through acceptable germination and shattering resistance of the mutant genotypes of E. lagascae . This is the first report of light treatment that significantly improved seed germination of E. lagascae , which may enhance efforts in the development of this new industrial crop as a feedstock for vernolic acid production., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Dr. Rene Van Acker reports financial support was provided by Ontario Ministry of Agriculture Food and Rural Affairs. None., (© 2024 Published by Elsevier Ltd.)

Background: The potential of plant-based sources of vernolic acid to provide agricultural producers with a market diversification opportunity and industrial manufacturers with a renewable, environmentally friendly chemical feedstock is immense. The herbaceous wild spurge or caper spurge (Euphorbia lagascae Spreng) is the most promising source of vernolic acid, containing an average oil content of 50%, of which around 60% is vernolic acid. Its seed yield ranges between 500 and 2000 kg ha -1 , and a theoretical yield of 180 kg ha -1 of pure vernolic acid is possible. The objective of this research was to characterize the flower and whole plant morphology so to allow for the development of a method to efficiently hybridize E. lagasce plants for breeding purposes., Results: In this study, we have characterized the flower and whole plant morphology in detail, thereby, developing an efficient method for hybridization of E. lagasce to allow for its breeding and improvement as a novel oil crop. Such method was not described previously in the literature making it difficult to breed this crop. We believe that the method will be of great value to plant breeders working on optimizing the crop, particularly in terms of the development of non-shattering cultivars with enhanced germination potential., Conclusions: The successful development of this crop through plant breeding could provide substantial economic benefits to farmers by offering them a new industrial oilseed crop. This research could prove invaluable in unlocking the potential of E. lagasce, and in turn, the potential of vernolic acid as a renewable, environmentally friendly source of chemical feedstock., (© 2024. The Author(s).)

In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Mohsen Yoosefzadeh-Najafabadi, Francois Belzile, Istvan Rajcan, Ashkan Golshani, and His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada for the contribution of Siwar Haidar, Simon Lackey, Martin Charette, A. Claire Cahagan, Thomas Hotte, Malcolm J. Morrison, Elroy R. Cober, and Samanfar Bahram.)

Soybean ( Glycine max L.) is an important food-grade strategic crop worldwide because of its high seed protein and oil contents. Due to the negative correlation between seed protein and oil percentage, there is a dire need to detect reliable quantitative trait loci (QTL) underlying these traits in order to be used in marker-assisted selection (MAS) programs. Genome-wide association study (GWAS) is one of the most common genetic approaches that is regularly used for detecting QTL associated with quantitative traits. However, the current approaches are mainly focused on estimating the main effects of QTL, and, therefore, a substantial statistical improvement in GWAS is required to detect associated QTL considering their interactions with other QTL as well. This study aimed to compare the support vector regression (SVR) algorithm as a common machine learning method to fixed and random model circulating probability unification (FarmCPU), a common conventional GWAS method in detecting relevant QTL associated with soybean seed quality traits such as protein, oil, and 100-seed weight using 227 soybean genotypes. The results showed a significant negative correlation between soybean seed protein and oil concentrations, with heritability values of 0.69 and 0.67, respectively. In addition, SVR-mediated GWAS was able to identify more relevant QTL underlying the target traits than the FarmCPU method. Our findings demonstrate the potential use of machine learning algorithms in GWAS to detect durable QTL associated with soybean seed quality traits suitable for genomic-based breeding approaches. This study provides new insights into improving the accuracy and efficiency of GWAS and highlights the significance of using advanced computational methods in crop breeding research.

Cinnamate 4-hydroxylase (C4H) is the first key cytochrome P450 monooxygenase (P450) enzyme in the phenylpropanoid pathway. It belongs to the CYP73 family of P450 superfamily, and catalyzes the conversion of trans-cinnamic acid to p-coumaric acid. Since p-coumaric acid serves as the precursor for the synthesis of a wide variety of metabolites involved in plant development and stress resistance, alteration in the expression of soybean C4H genes is expected to affect the downstream metabolite levels, and its ability to respond to stress. In this study, we identified four C4H genes in the soybean genome that are distributed into both class I and class II CYP73 family. GmC4H2, GmC4H14 and GmC4H20 displayed tissue- and developmental stage-specific gene expression patterns with their transcript accumulation at the highest level in root tissues. GmC4H10 appears to be a pseudogene as its transcript was not detected in any soybean tissues. Furthermore, protein homology modelling revealed substrate docking only for GmC4H2, GmC4H14 and GmC4H20. To demonstrate the function of GmC4Hs, we modified a cloning vector for the heterologous expression of P450s in yeast, and used it for microsomal protein production and enzyme assay. Our results confirmed that GmC4H2, GmC4H14 and GmC4H20 contain the ability to hydroxylate trans-cinnamic acid with varying efficiencies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Khatri et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.

Key Message: rAMP-seq based genomic selection for agronomic traits has been shown to be a useful tool for winter wheat breeding programs by increasing the rate of genetic gain. Genomic selection (GS) is an effective strategy to employ in a breeding program that focuses on optimizing quantitative traits, which results in the ability for breeders to select the best genotypes. GS was incorporated into a breeding program to determine the potential for implementation on an annual basis, with emphasis on selecting optimal parents and decreasing the time and costs associated with phenotyping large numbers of genotypes. The design options for applying repeat amplification sequencing (rAMP-seq) in bread wheat were explored, and a low-cost single primer pair strategy was implemented. A total of 1870 winter wheat genotypes were phenotyped and genotyped using rAMP-seq. The optimization of training to testing population size showed that the 70:30 ratio provided the most consistent prediction accuracy. Three GS models were tested, rrBLUP, RKHS and feed-forward neural networks using the University of Guelph Winter Wheat Breeding Program (UGWWBP) and Elite-UGWWBP populations. The models performed equally well for both populations and did not differ in prediction accuracy (r) for most agronomic traits, with the exception of yield, where RKHS performed the best with an r = 0.34 and 0.39 for each population, respectively. The ability to operate a breeding program where multiple selection strategies, including GS, are utilized will lead to higher efficiency in the program and ultimately lead to a higher rate of genetic gain., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Fast-paced yield improvement in strategic crops such as soybean is pivotal for achieving sustainable global food security. Precise genomic selection (GS), as one of the most effective genomic tools for recognizing superior genotypes, can accelerate the efficiency of breeding programs through shortening the breeding cycle, resulting in significant increases in annual yield improvement. In this study, we investigated the possible use of haplotype-based GS to increase the prediction accuracy of soybean yield and its component traits through augmenting the models by using sophisticated machine learning algorithms and optimized genetic information. The results demonstrated up to a 7% increase in the prediction accuracy when using haplotype-based GS over the full single nucleotide polymorphisms-based GS methods. In addition, we discover an auspicious haplotype block on chromosome 19 with significant impacts on yield and its components, which can be used for screening climate-resilient soybean genotypes with improved yield in large breeding populations., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

Drought stress significantly limits soybean [ Glycine max (L.) Merr.] yields in Ontario, Canada. Many studies of genetic variation for drought tolerance compare commercial lines with exotic, unadapted germplasm. We hypothesized that even current commercial cultivars adapted to Ontario would differ significantly for traits related to drought tolerance. In a greenhouse experiment, we grew fifteen soybean cultivars in field soil amended with sand in 1-m rooting columns, which allowed for simulation of field-like soil water profiles and rooting depths. Two watering treatments were imposed from the first flower until maturity by daily restoration of soil water to either 100% (control), or 50% (drought stress) of the maximum soil water holding capacity. Throughout the experiment, we measured volumetric soil water content at different depths in the soil profile, but found no evidence at any developmental stage that the cultivars differed for their ability to extract soil water from different depths. Drought stress reduced seed yield by 51% on average. Similar to the effects of drought in the field, pod number was the yield component most affected, with effects on seeds per pod and single-seed weight being comparatively minor. There were significant cultivar × treatment interactions for seed yield, pod number, shoot dry matter, and water use. We identified two drought-sensitive ( Saska and OAC Drayton ) and three drought-tolerant ( OAC Lakeview , OAC Champion , and PRO 2715R ) cultivars based on their ratios of seed yield under drought stress to seed yield under control conditions (seed yield ratio, SYR). Regression and principal component analyses revealed that drought-tolerant (high-SYR) cultivars were consistently those that maintained relatively high values for water use, biomass accumulation and pod number under drought stress; high water use efficiency under drought stress was also associated with a high SYR. One of the cultivars, OAC Lakeview , displayed a distinct mode of drought tolerance, maintaining a very high fraction of its control pod number under drought stress. This study helps define the physiological basis of soybean cultivar differences in drought tolerance, and provides direction for soybean breeders to select traits that could improve yield under drought stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Gebre, Rajcan and Earl.)

Competing Interests: Author MV was employed by PawCo Foods. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.